Table 2.

Characteristics of the studies selected for the meta-analysis (the samples origin continent: Asia, America, or Europe; type of samples: bronchoalveolar lavage (BAL), sputum, sputum (induced), lower airways (LA), upper airways (UA); the NGS sequencing method: 454 pyrosequencing for Pyrosequencing such as 454 FLX (Roche${}^{\mathrm{\copyright }}$), Illumina for bridge amplification such as MiSeq or HiSeq (Illumina${}^{\mathrm{\copyright }}$), 454 pyrosequencing/Illumina for combined methods, PacBio/Illumina for long read sequencing such as PacBio (Pacific Biosciences${}^{\mathrm{\copyright }}$) combined with Illumina, Other for the other combinations; the use of rarefaction analysis: YES or NO/NC (no or not stated clearly); the taxonomic level used: OTU or Genus (for OTU clustered at genus level); ASVs- vs

Study	Disease	Continent	Type of sample	NGS sequencing	Rarefaction	Level	ASV method	Design	$n_0$	$n_1$	Score
Goleva et al. [28]	Asthma	America	BAL	454 pyrosequencing	YES	Genus	NO ASV	Case-control	12	39	6
Denner et al. [29]	Asthma	America	BAL	Illumina	YES	Genus	NO ASV	Case-control	19	39	6
Sverrild et al. [30]	Asthma	Europe	BAL	Illumina	NO/NC	OTU	NO ASV	Case-control	10	23	5
Liu et al. [31]	Asthma	Asia	Sputum	Other	YES	OTU	NO ASV	Case-control	29	116	6
Li et al. [32]	Asthma	Asia	Sputum (induced)	454 pyrosequencing	NO/NC	OTU	NO ASV	Case-control	15	24	6
									15	25
									24	25
Marri et al. [33]	Asthma	America	Sputum (induced)	454 pyrosequencing	YES	OTU	NO ASV	Case-control	10	10	4
Huang et al. [34]	Asthma	Asia	Sputum (induced)	Illumina	YES	OTU	NO ASV	Case-control	16	22	6
Munck et al. [35]	Asthma	Europe	Sputum (induced)	454 pyrosequencing	YES	OTU	NO ASV	Case-control	20	44	6
Park et al. [36]	Asthma	Asia	UA	454 pyrosequencing	YES	Genus	NO ASV	Case-control	12	18	5
Lee et al. [20]	Asthma	Asia	UA	454 pyrosequencing/	NO/NC	OTU	NO ASV	Case-control	20	59	6
				Illumina
Erb-Downward et al. [37]	COPD	America	BAL	454 pyrosequencing	NO/NC	OTU	NO ASV	Case-control	10	4	5
Pragman et al. [38]	COPD	America	BAL	454 pyrosequencing	YES	OTU	NO ASV	Case-control	10	22	5
Einarsson et al. [39]	COPD	Europe	LA	Illumina	NO/NC	OTU	NO ASV	Case-control	19	18	6
Kim et al. [40]	COPD	Asia	LA	454 pyrosequencing	YES	OTU	NO ASV	Case-control	13	13	6
Feigelman et al. [25]	COPD	Europe	Sputum	Illumina	NO/NC	Genus	ASV	Case-control	4	4	5
Millares et al. [41]	COPD	Europe	Sputum	454 pyrosequencing	NO/NC	OTU	NO ASV	Cross-sectional	8	8	4
Wang et al. [21]	COPD	Asia	Sputum (induced)	PacBio/Illumina	YES	OTU	ASV	Case-control	27	98	6
Park et al. [36]	COPD	Asia	UA	454 pyrosequencing	YES	Genus	NO ASV	Case-control	12	17	5
Pletcher et al. [42]	CF	America	LA	Illumina	YES	OTU	NO ASV	Case-control	17	9	5
Soret et al. [43]	CF	Europe	Sputum	454 pyrosequencing	YES	OTU	NO ASV	Case-control	16	17	5
Narayanamurthy et al. [44]	CF	America	Sputum	Illumina	NO/NC	Genus	NO ASV	Case-control	8	16	5
Filkins et al. [26]	CF	America	Sputum	454 pyrosequencing	NO/NC	Genus	NO ASV	Cross-sectional	22	13	6
Coburn et al. [45]	CF	America	Sputum	Illumina	YES	OTU	NO ASV	Cross-sectional	100	27	6
Carmody et al. [27]	CF	America	Sputum	454 pyrosequencing	YES	OTU	NO ASV	Self-controlled	34	34	6
Byun et al. [46]	NCFB	Asia	BAL	Other	NO/NC	Genus	NO ASV	Cross-sectional	8	6	3

OTUs-based approaches: ASV or No ASV; the study design; control group sample size ($n_0$); case group sample size ($n_1$); and the quality score)